Clay

(credit: Wikimedia Commons)

What is it?

Clay is a minimalistic Clojure tool for data visualization and literate programming, compatible with the Kindly convention.

Also see the Babashka Conf 2023 talk.

Goals

• Easily explore & share things for others to easily pick & use.
• Encourage writing Kindly-compatible notes for future compatiblity with other tools.
• Flow with the REPL: encourage user interactions that flow naturally with the typical use of Clojure in editors and REPLs.

Setup

For rendering documents like this one with Clay, you need to:

• add kindly-default and Clay as dependencies
• call (kindly-default/setup!) and (clay/start!) (see below)

To enjoy Clay's dynamic interaction, you also need to inform it about code evaluations. This requires some setup at the your editor.

See the suggested setup for popular editors below. If your favourite editor is not supported yet, let us talk and make it work.

VSCode Calva

(to be updated soon)

Please add the following command to your keybindings.json file at the VScode setup (you may pick another key, of course). This command would evaluate a piece of code and send the result to be visualized in Clay.

{
"key": "ctrl+shift+enter",
"command": "calva.runCustomREPLCommand",
"args": "(scicloj.clay.v2.api/handle-form! (quote $current-form))"
}

Emacs CIDER

(to be updated soon)

Please load clay.el at your Emacs config.

It offers the following functions, that you may wish to create keybindings for:

IntelliJ Cursive

Under preferences, search for "REPL Commands" (or use the menu IntelliJ -> Preferences -> Languages and Frameworks -> Clojure -> REPL Commands)

Then add a global command, and edit it with these settings:

It is useful to add 3 commands:

• (scicloj.clay.v2.api/handle-form! (quote ~top-level-form))
• (scicloj.clay.v2.api/handle-form! (quote ~form-before-caret))
• (scicloj.clay.v2.api/show-namespace-and-write-html! "~file-path")

You can then add keybindings under Preferences -> Keymap for the new commands.

See the Cursive documentation on REPL commands and substitutions for more details.

Starting a Clay namespace

Now, we can write a namespace and play with Clay.

(ns index
  (:require [scicloj.clay.v2.api :as clay]
            [scicloj.kindly.v3.api :as kindly]
            [scicloj.kindly.v3.kind :as kind]
            [scicloj.kindly-default.v1.api :as kindly-default]))

(defonce memoized-slurp
  (memoize slurp))

nil

Initialize Kindly's default.

(kindly-default/setup!)

:ok

Let us start Clay.

(clay/start!)

(clay/swap-options!
 assoc
 :remote-repo {:git-url "https://github.com/scicloj/clay"
               :branch "main"})

:ok

These initializations can also be done in a user.clj file, making them available for all namespaces in the project. The browser view should open automatically.

A few useful actions

Showing the whole namespace:

(comment
  (clay/show-doc! "notebooks/index.clj"))

Writing the document:

(comment
  (clay/show-doc-and-write-html!
   "notebooks/index.clj"
   {:toc? true}))

Reopening the Clay view in the browser (in case you closed the browser tab previously opened by clay/start!)

(comment
  (clay/browse!))

These can be conveniently bound to functions and keys at your editor (to b documented soon).

Interaction

Clay responds to user evaluations by displaying the result visually.

(+ 1111 2222)

3333

In Emacs CIDER, after evaluation of a form (or a region), the browser view should show the evaluation result. In VSCode Calva, a similar effect can be achieved using the dedicated command and keybinding defined above.

Kinds

The way things should be visualized is determined by the advice of Kindly. In this namespace we demonstrate Kindly's default advice. User-defined Kindly advices should work as well. Kindly advises tools (like Clay) about the kind of way a given context should be displayed, by assigning to it a so-called kind. Please refer to the Kindly documentation for details about specifying and using kinds.

Examples

Plain values

By default, when there is no kind information provided by Kindly, values are simply pretty-printed.

(+ 4 5)

9

(str "abcd" "efgh")

"abcdefgh"

Hiccup

Hiccup, a popular Clojure way to represent HTML, can be specified by kind:

(kind/hiccup
 [:ul
  [:li [:p "hi"]]
  [:li [:big [:big [:p {:style ; https://www.htmlcsscolor.com/hex/7F5F3F
                        {:color "#7F5F3F"}}
                    "hello"]]]]])

As we can see, this kind is displayed by converting Hiccup to HTML.

Markdown

Markdown text (a vector of strings) can be handled using a kind too.

(kind/md
 ["
* This is [markdown](https://www.markdownguide.org/).
  * *Isn't it??*"
  "
* Here is **some more** markdown."])

As we can see, this kind is displayed by converting Hiccup to HTML.

Images

Java BufferedImage objects are displayed as images.

(import javax.imageio.ImageIO
        java.net.URL)

java.net.URL

(defonce clay-image
  (->  "https://upload.wikimedia.org/wikipedia/commons/2/2c/Clay-ss-2005.jpg"
       (URL.)
       (ImageIO/read)))

nil

clay-image

Plain data structures

Plain data structures (lists and sequnces, vectors, sets, maps) are pretty printed if there isn't any value inside which needs to be displayed in special kind of way.

(def people-as-maps
  (->> (range 29)
       (mapv (fn [i]
               {:preferred-language (["clojure" "clojurescript" "babashka"]
                                     (rand-int 3))
                :age (rand-int 100)}))))

(def people-as-vectors
  (->> people-as-maps
       (mapv (juxt :preferred-language :age))))

(take 5 people-as-maps)

({:preferred-language "clojurescript", :age 3}
 {:preferred-language "clojure", :age 84}
 {:preferred-language "babashka", :age 6}
 {:preferred-language "clojurescript", :age 19}
 {:preferred-language "clojure", :age 66})

(take 5 people-as-vectors)

(["clojurescript" 3]
 ["clojure" 84]
 ["babashka" 6]
 ["clojurescript" 19]
 ["clojure" 66])

(->> people-as-vectors
     (take 5)
     set)

#{["clojure" 66]
  ["babashka" 6]
  ["clojurescript" 19]
  ["clojure" 84]
  ["clojurescript" 3]}

When something inside needs to be displayed in a special kind of way, the data structures are printed in a way that makes that clear.

(def nestes-structure-1
  {:vector-of-numbers [2 9 -1]
   :vector-of-different-things ["hi"
                                (kind/hiccup
                                 [:big [:big "hello"]])]
   :map-of-different-things {:markdown (kind/md ["*hi*, **hi**"])
                             :number 9999}
   :hiccup (kind/hiccup
            [:big [:big "bye"]])})

nestes-structure-1

Pretty printing

The :kind/pprint kind makes sure to simply pretty-print values:

(kind/pprint nestes-structure-1)

{:vector-of-numbers [2 9 -1],
 :vector-of-different-things ["hi" [:big [:big "hello"]]],
 :map-of-different-things {:markdown ["*hi*, **hi**"], :number 9999},
 :hiccup [:big [:big "bye"]]}

Datasets

tech.ml.dataset datasets currently use the default printing of the library, Let us create such a dataset using Tablecloth.

(require '[tablecloth.api :as tc])

nil

(-> {:x (range 6)
     :y [:A :B :C :A :B :C]}
    tc/dataset)

(-> {:x [1 [2 3] 4]
     :y [:A :B :C]}
    tc/dataset)

(-> [{:x 1 :y 2 :z 3}
     {:y 4 :z 5}]
    tc/dataset)

(-> people-as-maps
    tc/dataset)

Tables

The :kind/table kind can be handy for an interactive table view.

(kind/table
 {:column-names [:preferred-language :age]
  :row-vectors people-as-vectors})

(kind/table
 {:column-names [:preferred-language :age]
  :row-maps people-as-maps})

(kind/table
 {:column-names [:preferred-language :age]
  :row-maps (take 5 people-as-maps)})

(-> people-as-maps
    tc/dataset
    kind/table)

Vega and Vega-Lite

(defn vega-lite-point-plot [data]
  (-> {:data {:values data},
       :mark "point"
       :encoding
       {:size {:field "w" :type "quantitative"}
        :x {:field "x", :type "quantitative"},
        :y {:field "y", :type "quantitative"},
        :fill {:field "z", :type "nominal"}}}
      kind/vega-lite))

(defn random-data [n]
  (->> (repeatedly n #(- (rand) 0.5))
       (reductions +)
       (map-indexed (fn [x y]
                      {:w (rand-int 9)
                       :z (rand-int 9)
                       :x x
                       :y y}))))

(defn random-vega-lite-plot [n]
  (-> n
      random-data
      vega-lite-point-plot))

(random-vega-lite-plot 9)

Cytoscape.js

(def cytoscape-example
  {:elements {:nodes [{:data {:id "a" :parent "b"} :position {:x 215 :y 85}}
                      {:data {:id "b"}}
                      {:data {:id "c" :parent "b"} :position {:x 300 :y 85}}
                      {:data {:id "d"} :position {:x 215 :y 175}}
                      {:data {:id "e"}}
                      {:data {:id "f" :parent "e"} :position {:x 300 :y 175}}]
              :edges [{:data {:id "ad" :source "a" :target "d"}}
                      {:data {:id "eb" :source "e" :target "b"}}]}
   :style [{:selector "node"
            :css {:content "data(id)"
                  :text-valign "center"
                  :text-halign "center"}}
           {:selector "parent"
            :css {:text-valign "top"
                  :text-halign "center"}}
           {:selector "edge"
            :css {:curve-style "bezier"
                  :target-arrow-shape "triangle"}}]
   :layout {:name "preset"
            :padding 5}})

(kind/cytoscape cytoscape-example)

(kind/cytoscape [cytoscape-example
                 {:style {:height 100
                          :width 100}}])

Apache Echarts

(kind/echarts
 {:xAxis {:data ["Mon" "Tue" "Wed" "Thu" "Fri" "Sat" "Sun"]}
  :yAxis {}
  :series [{:type "bar"
            :color ["#7F5F3F"]
            :data [23 24 18 25 27 28 25]}]})

MathBox.cljs

inspired by the official MathBox.cljs tutorial

(kind/hiccup
 '[(let [Data (fn []
                [mathbox.primitives/Interval
                 {:expr (fn [emit x _i t]
                          (emit x (Math/sin (+ x t))))
                  :width 64
                  :channels 2}])
         Curve (fn []
                 [:<>
                  [Data]
                  [mathbox.primitives/Line {:width 5
                                            :color "#3090FF"}]])
         Main (fn []
                [mathbox.core/MathBox
                 {:container {:style {:height "400px" :width "100%"}}
                  :focus 3}
                 [mathbox.primitives/Camera {:position [0 0 3]
                                             :proxy true}]
                 [mathbox.primitives/Cartesian
                  {:range [[-2 2] [-1 1]]
                   :scale [2 1]}
                  [mathbox.primitives/Axis {:axis 1 :width 3 :color "black"}]
                  [mathbox.primitives/Axis {:axis 2 :width 3 :color "black"}]
                  [mathbox.primitives/Grid {:width 2 :divideX 20 :divideY 10}]
                  [Curve]]])
         *state (r/atom {:open? false})]
     (fn []
       [:div
        [:button {:on-click #(swap! *state update :open? not)}
         (if (:open? @*state)
           "close"
           "open")]
        (when (:open? @*state)
          [Main])]))])

plotly

(kind/hiccup
 '[plotly
   {:data [{:x [0 1 3 2]
            :y [0 6 4 5]
            :z [0 8 9 7]
            :type :scatter3d
            :mode :lines+markers
            :opacity 0.5
            :line {:width 5}
            :marker {:size 4
                     :colorscale :Viridis}}]}])

Katex

(kind/hiccup
 '[katex "1+x^2"])

Emmy

(kind/hiccup
 '(require '[emmy.env :as e :refer [D]]))

(kind/hiccup
 [:div
  '(-> 'x
       ((D e/cube))
       e/simplify
       e/->infix)])

(kind/hiccup
 '[katex
   (-> 'x
       ((D e/cube))
       e/simplify
       e/->infix)])

tmdjs

(kind/hiccup
 '(require '[tech.v3.dataset :as tmd]))

(kind/hiccup
 '[(fn []
     [:div
      (-> {:x [1 2 3]}
          tmd/->dataset
          :x
          pr-str)])])

3dmol

(experimental)

(kind/hiccup
 ['three-d-mol-viewer
  {:data-pdb "2POR"}])

(kind/hiccup
 ['(fn [{:keys [pdb-data]}]
     [:div
      {:style {:width "100%"
               :height "500px"
               :position "relative"}
       :ref (fn [el]
              (let [config (clj->js
                            {:backgroundColor "0xffffff"})
                    viewer (.createViewer js/$3Dmol el #_config)]
                (.setViewStyle viewer (clj->js
                                       {:style "outline"}))
                (.addModelsAsFrames viewer pdb-data "pdb")
                (.addSphere viewer (clj->js
                                    {:center {:x 0
                                              :y 0
                                              :z 0}
                                     :radius 1
                                     :color "green"}))
                (.zoomTo viewer)
                (.render viewer)
                (.zoom viewer 0.8 2000)))}
      ;; need to keep this symbol to let Clay infer the necessary dependency
      'three-d-mol])
  {:pdb-data (memoized-slurp "https://files.rcsb.org/download/2POR.pdb")}])

Leaflet

(kind/hiccup
 ['(fn []
     [:div
      {:style {:width "100%"
               :height "500px"}
       :ref (fn [el]
              (let [m (-> js/L
                          (.map el)
                          (.setView (clj->js [52.5274319 13.4004289])
                                    19))]
                (-> js/L
                    (.tileLayer "https://tile.openstreetmap.org/{z}/{x}/{y}.png"
                                (clj->js {:maxZoom 19
                                          :attribution "© OpenStreetMap"}))
                    (.addTo m))))}
      'leaflet])])

Delays

Clojure Delays are a common way to define computations that do not take place immediately. The computation takes place when dereferencing the value for the first time. Clay makes sure to dererence Delays when passing values for visualization. This is handy for slow example snippets and explorations, that one would typically not like to slow down the evaluation of the whole namespace, but would like to visualize them on demand and also include in them in the final document.

(delay
  (Thread/sleep 500)
  (+ 1 2))

3

(delay
  [:div [:big "hi......."]])

[:div [:big "hi......."]]